New mechanisms for stratification and upwelling in the southern Great Barrier Reef (GBR) are identified, and dynamic details of Capricorn Eddy, a transient feature located off the shelf at the southern extremity of the GBR, are revealed using the newly available surface current from High Frequency (HF) radar combined with other remote sensing and mooring data. The HF radar surface currents were used for tidal harmonic analysis and current-wind correlation analysis. These analyses, combined with Sea Surface Temperature (SST) data, mooring data, and altimetry-based geostrophic currents, enabled the effects of forcing from the large-scale oceanic currents (including the East Australian Current (EAC)), wind, and tides in a topographically complex flow regime to be separately identified. Within the indentation region where the width of the shelf abruptly narrows, current is strongly coupled with the EAC. Here strong residual flows, identified on current maps and SST images, fall into three patterns: southward flow, northwestward flow, and an eddy. Multiple data sets shed light on the prerequisite for the formation of the eddy, the reasons for its geometric variation, and its evolution with time. Intrusions of the eddy onto the shelf result in stratification characterized by a significant increase of surface temperature. Upwelling driven by wind or oceanic inflow is shown to cause stratification of previously well-mixed shelf water. The upwelling appears to be associated with equatorward-traveling coastal-trapped waves. The integrative method of analysis embodied here is applicable to other coastal regions with complex circulation.